BioExcel Centre of Excellence for ComputationalBiomolecular Research

Deliverables

Public release of all current code development within the project, with accompanying documentation, tests, benchmarks, and benchmark reports.

First release of demonstration workflows

This deliverable will cover the first release of demonstration workflows. It will include an update of the initial roadmap.

Project release of core applications

Public release of all current code development within the project, with accompanying documentation, tests, benchmarks, and benchmark reports.

Final release of demonstration workflows

This deliverable will present in detail the demonstration workflows implemented, including feedback considerations, usability, availability and results.

Development of a framework for the combination of HPC and HPDA operations

Report on the design and development of initial workflows combining HPC and HPDA operations

Best Practice Guides

A collection of best practices developed for the core project codes and related work in T34

Quality assurance and risk management plan

This deliverable will discuss the overall quality monitoring process for the project (such as deliverables and milestone completion, KPIs) and the overall risk management strategy. The risks will be regularly assessed in the mandatory management reports.

Updated specification of development process

A report specifying the software engineering testing and quality assurance aspects of the project building on past efforts and adapting them to new codes and changed contexts This will also include a report of the BioExcel CP2K profiling outcome

Business Model design report

Detailed BioExcel Business Model for taking the project into a sustainability phase

Provision of a Workflow Environment at BioExcel portal

Report on the updates implemented in the BioExcel Cloud Portal

Integration of BioExcel software framework with standards and international initiatives

The deliverable will detail the integration of BioExcel computational framework with external initiatives like ELIXIR GA4GH

Update of whitepaper on scientific software development

Publication of an updated version of the scientific software development white paper published by the first BioExcel project This should reflect the current state of software development of the BioExcel codes as well updates to reflect changes in software development standards

Exascale co-design benchmark cases

Key kernels from the core applications will be extracted to become useful to vendor or tool implementers as optimization targets

Updated software roadmaps

The roadmap for each of the core applications will be updated for new changes to HPC hardware and software contexts user requests and progress since previous roadmaps

Work Plans for UCs

This deliverable will contain the detailed workplans for the use cases

Branding and Quality Mark Design Inception Report

An initial document setting the vision for the CoE brand as a European Centre promoting quality

Pre-Exascale showcase calculation and Use Case Final Report

A large preExascale showcase calculation will be performed and analysed This deliverable will also include a final report on the work undertaken on the projects use cases

User Community Support and Engagement Report (final)

An update to D34 to include work from the second half of the project in the same areas as D34 along with a summary of feedback from the CAPRI workshop or relevant T36 work

Annotated and justified Service Catalogue

A first list of exploitable assets identified

Management Plan

Initial deliverable stating the management organization and planning for the entire project

Dissemination and outreach plan

This document will outline the overall plan for dissemination and outreach activities of the CoE

State-of-the-art and Initial Roadmap

This deliverable will summarise and describe the new technologies, methods and tools identified and collected to be used in the project workflows. From these, an initial roadmap will be proposed.

User Community Support and Engagement Report (half-time update)

Reports from events community support engagement activities and summary of feedback provided to the rest of the project This report will also include results and analysis of the first and second user surveys

Final report on dissemination and training

Report on the status and outcome of the disseminationoutreach activities and the training programme during the second half of the project

Long-term hardware and application roadmap

The roadmap for each of the core applications will be related to what has been achieved in BioExcel2 and updated for new changes to HPC hardware and software contexts user requests and progress since previous roadmaps An update to D13

High Performance Computing in support of COVID-19 Research

Description of BioExcels work in the global efforts against Covid19

Use Case Progress Report

An update on the progress of the use cases

Progress report and update on training and dissemination plan

This document will report on the status and outcome of the dissemination/outreach activities and the training programme. Additionally, it will present updated plans for the second half of the project.

First release of workflow-ready building blocks library

This deliverable will describe the design and development of the first release of the building blocks library.

Training Plan

This document will include a report of the updated competency profile, an evaluation of the virtual training pilots, and outline of the BioExcel Training programme.

Data Management Plan

The data management plan for the use cases

Publications

The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry

Author(s): Montserrat Terrazas, Vito Genna, Guillem Portella, Núria Villegas, Dani Sánchez, Carme Arnan, Carlos Pulido-Quetglas, Rory Johnson, Roderic Guigó, Isabelle Brun-Heath, Anna Aviñó, Ramon Eritja, Modesto Orozco
Published in: Chem, Issue 5/6, 2019, Page(s) 1619-1631, ISSN 2451-9294
Publisher: Elsevier
DOI: 10.1016/j.chempr.2019.04.002

A molecular mechanism for transthyretin amyloidogenesis

Author(s): Ai Woon Yee, Matteo Aldeghi, Matthew P. Blakeley, Andreas Ostermann, Philippe J. Mas, Martine Moulin, Daniele de Sanctis, Matthew W. Bowler, Christoph Mueller-Dieckmann, Edward P. Mitchell, Michael Haertlein, Bert L. de Groot, Elisabetta Boeri Erba, V. Trevor Forsyth
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-08609-z

Computational approaches to therapeutic antibody design: established methods and emerging trends

Author(s): Richard A Norman, Francesco Ambrosetti, Alexandre M J J Bonvin, Lucy J Colwell, Sebastian Kelm, Sandeep Kumar, Konrad Krawczyk
Published in: Briefings in Bioinformatics, 2019, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbz095

LightDock goes information-driven

Author(s): Jorge Roel-Touris, Alexandre M J J Bonvin, Brian Jiménez-García
Published in: Bioinformatics, Issue 36/3, 2019, Page(s) 950-952, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz642

Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3

Author(s): Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin
Published in: Journal of Computer-Aided Molecular Design, Issue 33/1, 2019, Page(s) 83-91, ISSN 0920-654X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10822-018-0148-4

An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45

Author(s): Panagiotis I. Koukos, Jorge Roel‐Touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael E. Trellet, Adrien S. J. Melquiond, Li C. Xue, Rodrigo V. Honorato, Irina Moreira, Zeynep Kurkcuoglu, Anna Vangone, Alexandre M. J. J. Bonvin
Published in: Proteins: Structure, Function, and Bioinformatics, Issue 88/8, 2020, Page(s) 1029-1036, ISSN 0887-3585
Publisher: Wiley-Liss Inc
DOI: 10.1002/prot.25869

Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond

Author(s): Alexandra Balaceanu, Diana Buitrago, Jürgen Walther, Adam Hospital, Pablo D Dans, Modesto Orozco
Published in: Nucleic Acids Research, Issue 47/9, 2019, Page(s) 4418-4430, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz255

Molywood: streamlining the design and rendering of molecular movies

Author(s): Miłosz Wieczór, Adam Hospital, Genis Bayarri, Jacek Czub, Modesto Orozco
Published in: Bioinformatics, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa584

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Author(s): H.M. Berman, P,D. Adams, A.M.J.J. Bonvin, S.K. Burley, B. Carragher, W. Chiu, F. DiMaio, T.E. Ferrin, M.J. Gabanyi, T.D. Goddard, P.R. Griffin, J. Haas, C.A. Hanke, J.C. Hoch, G. Hummer, G. Kurisu, C.L. Lawson, A. Leitner, J.L. Markley, J. Meiler, G.T. Montelione, G.N. Phillips Jr., T. Prisner, J. Rappsilber, D.C. Schriemer, T. Schwede, C.A.M. Seidel, T.S. Strutzenberg, D.I. Svergun, E. Tajkhorshi
Published in: Structure, Issue 27/12, 2019, Page(s) 1745-1759, ISSN 2352-0124
Publisher: Elsevier Limited
DOI: 10.1016/j.str.2019.11.002

An In-Depth Look at DNA Crystals through the Prism of Molecular Dynamics Simulations

Author(s): Antonija Kuzmanic, Pablo D. Dans, Modesto Orozco
Published in: Chem, Issue 5/3, 2019, Page(s) 649-663, ISSN 2451-9294
Publisher: Elsevier
DOI: 10.1016/j.chempr.2018.12.007

A multifunctional toolkit for target-directed cancer therapy

Author(s): Montserrat Terrazas, Dani Sánchez, Federica Battistini, Núria Villegas, Isabelle Brun-Heath, Modesto Orozco
Published in: Chemical Communications, Issue 55/6, 2019, Page(s) 802-805, ISSN 1359-7345
Publisher: Royal Society of Chemistry
DOI: 10.1039/c8cc08823c

iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations

Author(s): Cunliang Geng, Anna Vangone, Gert E. Folkers, Li C. Xue, Alexandre M. J. J. Bonvin
Published in: Proteins: Structure, Function, and Bioinformatics, Issue 87/2, 2019, Page(s) 110-119, ISSN 0887-3585
Publisher: Wiley-Liss Inc
DOI: 10.1002/prot.25630

Natural helix 9 mutants of PPARγ differently affect its transcriptional activity

Author(s): Marjoleine F. Broekema, Maarten P.G. Massink, Cinzia Donato, Joep de Ligt, Joerg Schaarschmidt, Anouska Borgman, Marieke G. Schooneman, Diana Melchers, Martin N. Gerding, René Houtman, Alexandre M.J.J. Bonvin, Amit R. Majithia, Houshang Monajemi, Gijs W. van Haaften, Maarten R. Soeters, Eric Kalkhoven
Published in: Molecular Metabolism, Issue 20, 2019, Page(s) 115-127, ISSN 2212-8778
Publisher: Elsevier GmbH
DOI: 10.1016/j.molmet.2018.12.005

DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region

Author(s): Anna Cuppari, Pablo Fernández-Millán, Federica Battistini, Aleix Tarrés-Solé, Sébastien Lyonnais, Guillermo Iruela, Elena Ruiz-López, Yuliana Enciso, Anna Rubio-Cosials, Rafel Prohens, Miquel Pons, Carlos Alfonso, Katalin Tóth, Germán Rivas, Modesto Orozco, Maria Solà
Published in: Nucleic Acids Research, Issue 47/12, 2019, Page(s) 6519-6537, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz406

Modeling, Simulations, and Bioinformatics at the Service of RNA Structure

Author(s): Pablo D. Dans, Diego Gallego, Alexandra Balaceanu, Leonardo Darré, Hansel Gómez, Modesto Orozco
Published in: Chem, Issue 5/1, 2019, Page(s) 51-73, ISSN 2451-9294
Publisher: Elsevier
DOI: 10.1016/j.chempr.2018.09.015

Integrative Modelling of Biomolecular Complexes

Author(s): P.I. Koukos, A.M.J.J. Bonvin
Published in: Journal of Molecular Biology, Issue 432/9, 2020, Page(s) 2861-2881, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2019.11.009

Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase

Author(s): Leander Goldbach, Bram J. A. Vermeulen, Sami Caner, Minglong Liu, Christina Tysoe, Lieke van Gijzel, Ryoji Yoshisada, Mikael Trellet, Hugo van Ingen, Gary D. Brayer, Alexandre M. J. J. Bonvin, Seino A. K. Jongkees
Published in: ACS Chemical Biology, Issue 14/8, 2019, Page(s) 1751-1759, ISSN 1554-8929
Publisher: American Chemical Society
DOI: 10.1021/acschembio.9b00290

Pyruvate carboxylase deficiency type A and type C: Characterization of five novel pathogenic variants in PC and analysis of the genotype–phenotype correlation

Author(s): Emanuele G. Coci, Vytautas Gapsys, Natasha Shur, Yoon Shin‐Podskarbi, Bert L. Groot, Kathryn Miller, Jerry Vockley, Neal Sondheimer, Rebecca Ganetzky, Peter Freisinger
Published in: Human Mutation, Issue 40/6, 2019, Page(s) 816-827, ISSN 1059-7794
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/humu.23742

Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

Author(s): Viacheslav Bolnykh, Jógvan Magnus Haugaard Olsen, Simone Meloni, Martin P. Bircher, Emiliano Ippoliti, Paolo Carloni, Ursula Rothlisberger
Published in: Journal of Chemical Theory and Computation, Issue 15/10, 2019, Page(s) 5601-5613, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.9b00424

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Author(s): Christine Orengo, Sameer Velankar, Shoshana Wodak, Vincent Zoete, Alexandre M.J.J. Bonvin, Arne Elofsson, K. Anton Feenstra, Dietland L. Gerloff, Thomas Hamelryck, John M. Hancock, Manuela Helmer-Citterich, Adam Hospital, Modesto Orozco, Anastassis Perrakis, Matthias Rarey, Claudio Soares, Joel L. Sussman, Janet M. Thornton, Pierre Tuffery, Gabor Tusnady, Rikkert Wierenga, Tiina Salminen, Bohdan S
Published in: F1000Research, Issue 9, 2020, Page(s) 278, ISSN 2046-1402
Publisher: F1000 Research Ltd.
DOI: 10.12688/f1000research.20559.1

Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches

Author(s): Matteo Aldeghi, Vytautas Gapsys, Bert L. de Groot
Published in: ACS Central Science, Issue 5/8, 2019, Page(s) 1468-1474, ISSN 2374-7943
Publisher: ACS Central Science
DOI: 10.1021/acscentsci.9b00590

How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition

Author(s): Federica Battistini, Adam Hospital, Diana Buitrago, Diego Gallego, Pablo D. Dans, Josep Lluis Gelpí, Modesto Orozco
Published in: Journal of Molecular Biology, Issue 431/19, 2019, Page(s) 3845-3859, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2019.07.021

Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering.

Author(s): Marie Lycksell; Urska Rovsnik; Cathrine Bergh; Nicolai Tidemand Johansen; Anne L. Martel; Lionel Porcar; Lise Arleth; Rebecca J. Howard; Erik Lindahl; Erik Lindahl
Published in: 'Proceedings of the National Academy of Sciences ', vol: 118 , pages: e2108006118-1-e2108006118-9 (2021), Issue 75, 2021, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2108006118

The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

Author(s): Elin Claesson, Weixiao Yuan Wahlgren, Heikki Takala, Suraj Pandey, Leticia Castillon, Valentyna Kuznetsova, Léocadie Henry, Matthijs Panman, Melissa Carrillo, Joachim Kübel, Rahul Nanekar, Linnéa Isaksson, Amke Nimmrich, Andrea Cellini, Dmitry Morozov, Michał Maj, Moona Kurttila, Robert Bosman, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, So Iwata, Shigeki Owada, Keith Moffat, Gerrit
Published in: eLife, Issue 9, 2020, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.53514

Pre-exascale computing of protein-ligand binding free energies with open source software for drug design.

Author(s): Vytautas Gapsys; David F. Hahn; Gary Tresadern; David L. Mobley; Markus Rampp; Bert L. de Groot
Published in: Journal of Chemical Information and Modeling, Issue 62, 2021, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.1c01445

Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4

Author(s): Andrea Basciu, Panagiotis I. Koukos, Giuliano Malloci, Alexandre M. J. J. Bonvin, Attilio V. Vargiu
Published in: Journal of Computer-Aided Molecular Design, Issue 34/2, 2020, Page(s) 149-162, ISSN 0920-654X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10822-019-00244-6

The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules

Author(s): Pablo D Dans, Alexandra Balaceanu, Marco Pasi, Alessandro S Patelli, Daiva Petkevičiūtė, Jürgen Walther, Adam Hospital, Genís Bayarri, Richard Lavery, John H Maddocks, Modesto Orozco
Published in: Nucleic Acids Research, Issue 47/21, 2019, Page(s) 11090-11102, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz905

Surviving the deluge of biosimulation data

Author(s): Adam Hospital, Federica Battistini, Robert Soliva, Josep Lluis Gelpí, Modesto Orozco
Published in: WIREs Computational Molecular Science, Issue 10/3, 2020, ISSN 1759-0876
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/wcms.1449

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Author(s): Marc F. Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphaël A. G. Chaleil, Tereza Gerguri, Paul A. Bates, Elodie Laine, Alessandra Carbone, Sergei Grudinin, Ren Kong, Ran‐Ran Liu, Xi‐Ming Xu, Hang Shi, Shan Chang, Miriam Eisenstein, Agnieszka Karczynska, Cezary Czaplewski, Emilia Lubecka, Agnieszka Lipska, Paweł Krupa, Magdalena Mozolewska, Łukasz Golon, Sergey Samsonov,
Published in: Proteins: Structure, Function, and Bioinformatics, Issue 87/12, 2019, Page(s) 1200-1221, ISSN 0887-3585
Publisher: Wiley-Liss Inc
DOI: 10.1002/prot.25838

Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset

Author(s): Eddy Elisée, Vytautas Gapsys, Nawel Mele, Ludovic Chaput, Edithe Selwa, Bert L. de Groot, Bogdan I. Iorga
Published in: Journal of Computer-Aided Molecular Design, Issue 33/12, 2019, Page(s) 1031-1043, ISSN 0920-654X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10822-019-00232-w

Photoactive Yellow Protein Chromophore Photoisomerizes around a Single Bond if the Double Bond Is Locked

Author(s): Satu Mustalahti, Dmitry Morozov, Hoi Ling Luk, Rajanish R. Pallerla, Pasi Myllyperkiö, Mika Pettersson, Petri M. Pihko, Gerrit Groenhof
Published in: The Journal of Physical Chemistry Letters, Issue 11/6, 2020, Page(s) 2177-2181, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.0c00060

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape

Author(s): Andrea Basciu, Giuliano Malloci, Fabio Pietrucci, Alexandre M. J. J. Bonvin, Attilio V. Vargiu
Published in: Journal of Chemical Information and Modeling, Issue 59/4, 2019, Page(s) 1515-1528, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.8b00730

Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling

Author(s): Multamäki, Elina; Nanekar, Rahul; Morozov, Dmitry; Lievonen, Topias; Golonka, David; Wahlgren, Weixiao Yuan; Stucki-Buchli, Brigitte; Rossi, Jari; Hytönen, Vesa P.; Westenhoff, Sebastian; Ihalainen, Janne A.; Möglich, Andreas; Takala, Heikki
Published in: Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021), Issue 45, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

Author(s): O.M.H. Salo-Ahen, I. Alanko, R. Bhadane, A.M.J.J. Bonvin, R. Vargas Honorato, S. Hossain, A.H. Juffer, A. Kabedev, M. Lahtela-Kakkonen, A. Støttrup Larsen, E. Lescrinier, P. Marimuthu, M. Mirza, G. Mustafa, A. Nunes-Alves, T. Pantsar, A. Saadabadi, K. Singaravelu, M. Vanmeert.
Published in: Processes, Issue 9(1), 2021, Page(s) 71, ISSN 2227-9717
Publisher: MDPI
DOI: 10.3390/pr9010071

Mode of action of teixobactins in cellular membranes

Author(s): Rhythm Shukla, João Medeiros-Silva, Anish Parmar, Bram J. A. Vermeulen, Sanjit Das, Alessandra Lucini Paioni, Shehrazade Jekhmane, Joseph Lorent, Alexandre M. J. J. Bonvin, Marc Baldus, Moreno Lelli, Edwin J. A. Veldhuizen, Eefjan Breukink, Ishwar Singh, Markus Weingarth
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-16600-2

EXPLORING THE CONFORMATIONAL LANDSCAPE OF BIOACTIVE SMALL MOLECULES

Author(s): Sanja Zivanovic, Francesco Colizzi, David Moreno, Adam Hospital, Robert Soliva, Modesto Orozco
Published in: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c00304

Finding the ΔΔ G spot: Are predictors of binding affinity changes upon mutations in protein-protein interactions ready for it?

Author(s): Cunliang Geng, Li C. Xue, Jorge Roel-Touris, Alexandre M. J. J. Bonvin
Published in: Wiley Interdisciplinary Reviews: Computational Molecular Science, Issue 9/5, 2019, Page(s) e1410, ISSN 1759-0876
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/wcms.1410

An artificial DNAzyme RNA ligase shows a reaction mechanism resembling that of cellular polymerases

Author(s): Juan Aranda, Montserrat Terrazas, Hansel Gómez, Núria Villegas, Modesto Orozco
Published in: Nature Catalysis, Issue 2/6, 2019, Page(s) 544-552, ISSN 2520-1158
Publisher: Nature
DOI: 10.1038/s41929-019-0290-y

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

Author(s): Andrea Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen, Bert L. de Groot, Zoe Cournia, Alex Dickson, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera
Published in: Journal of Computer-Aided Molecular Design, Issue 34/5, 2020, Page(s) 601-633, ISSN 0920-654X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10822-020-00290-5

Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK

Author(s): Jorge Roel-Touris, Charleen G. Don, Rodrigo V. Honorato, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin
Published in: Journal of Chemical Theory and Computation, Issue 15/11, 2019, Page(s) 6358-6367, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.9b00310

Molecular Basis of CLC Antiporter Inhibition by Fluoride

Author(s): Maria Gabriella Chiariello, Viacheslav Bolnykh, Emiliano Ippoliti, Simone Meloni, Jógvan Magnus Haugaard Olsen, Thomas Beck, Ursula Rothlisberger, Christoph Fahlke, Paolo Carloni
Published in: Journal of the American Chemical Society, Issue 142/16, 2020, Page(s) 7254-7258, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.9b13588

Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor

Author(s): Albert Escobedo, Busra Topal, Micha B. A. Kunze, Juan Aranda, Giulio Chiesa, Daniele Mungianu, Ganeko Bernardo-Seisdedos, Bahareh Eftekharzadeh, Margarida Gairí, Roberta Pierattelli, Isabella C. Felli, Tammo Diercks, Oscar Millet, Jesús García, Modesto Orozco, Ramon Crehuet, Kresten Lindorff-Larsen, Xavier Salvatella
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-09923-2

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

Author(s): Yuriy Khalak; Gary Tresadern; Matteo Aldeghi; Hannah Magdalena Baumann; David L. Mobley; Bert L. de Groot; Vytautas Gapsys
Published in: CHemical Science, Issue 59, 2021, ISSN 2633-0679
Publisher: Royal Society of Chemistry
DOI: 10.26434/chemrxiv-2021-rxxbb

West-Life: A Virtual Research Environment for structural biology

Author(s): Chris Morris, Paolo Andreetto, Lucia Banci, Alexandre M.J.J. Bonvin, Grzegorz Chojnowski, Laura del Cano, José Marıa Carazo, Pablo Conesa, Susan Daenke, George Damaskos, Andrea Giachetti, Natalie E.C. Haley, Maarten L. Hekkelman, Philipp Heuser, Robbie P. Joosten, Daniel Kouřil, Aleš Křenek, Tomáš Kulhánek, Victor S. Lamzin, Nurul Nadzirin, Anastassis Perrakis, Antonio Rosato, Fiona Sander
Published in: Journal of Structural Biology: X, Issue 1, 2019, Page(s) 100006, ISSN 2590-1524
Publisher: Elsevier Inc.
DOI: 10.1016/j.yjsbx.2019.100006

BIOACTIVE CONFORMATIONAL ENSEMBLE SERVER AND DATABASE. A PUBLIC FRAMEWORK TO SPEED UP IN SILICO DRUG DISCOVERY

Author(s): Sanja Zivanovic, Genís Bayarri, Francesco Colizzi, David Moreno, Josep Lluis Gelpi, Robert Soliva, Adam Hospital, Modesto Orozco
Published in: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c00305

A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids

Author(s): Sebastian Arangundy-Franklin, Alexander I. Taylor, Benjamin T. Porebski, Vito Genna, Sew Peak-Chew, Alexandra Vaisman, Roger Woodgate, Modesto Orozco, Philipp Holliger
Published in: Nature Chemistry, Issue 11/6, 2019, Page(s) 533-542, ISSN 1755-4330
Publisher: Nature Publishing Group
DOI: 10.1038/s41557-019-0255-4

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.

Author(s): Federica Battistini; Pablo D. Dans; Pablo D. Dans; Montserrat Terrazas; Chiara Lara Castellazzi; Guillem Portella; Mireia Labrador; Núria Villegas; Isabelle Brun-Heath; Carlos González; Modesto Orozco
Published in: nlmid: 101238922, Issue 18, 2021, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.17863/cam.79747

VeriNA3d: an R package for nucleic acids data mining

Author(s): Diego Gallego, Leonardo Darré, Pablo D Dans, Modesto Orozco
Published in: Bioinformatics, Issue 35/24, 2019, Page(s) 5334-5336, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz553

Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics

Author(s): Francesco Colizzi, Adam Hospital, Sanja Zivanovic, Modesto Orozco
Published in: Angewandte Chemie International Edition, Issue 58/12, 2019, Page(s) 3759-3763, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201810922

Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors

Author(s): Tomas Bastys, Vytautas Gapsys, Hauke Walter, Eva Heger, Nadezhda T. Doncheva, Rolf Kaiser, Bert L. de Groot, Olga V. Kalinina
Published in: Retrovirology, Issue 17/1, 2020, ISSN 1742-4690
Publisher: BioMed Central
DOI: 10.1186/s12977-020-00520-6

Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems

Author(s): Zeynep Kurkcuoglu, Alexandre M. J. J. Bonvin
Published in: Proteins: Structure, Function, and Bioinformatics, Issue 88/2, 2019, Page(s) 292-306, ISSN 0887-3585
Publisher: Wiley-Liss Inc
DOI: 10.1002/prot.25802

Cyclization and Docking Protocol for Cyclic Peptide–Protein Modeling Using HADDOCK2.4

Author(s): Vicky Charitou; Siri C. van Keulen; Alexandre M. J. J. Bonvin
Published in: Crossref, Issue 78, 2022, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.2c00075

Large-scale prediction of binding affinity in protein–small ligand complexes: the PRODIGY-LIG web server

Author(s): Anna Vangone, Joerg Schaarschmidt, Panagiotis Koukos, Cunliang Geng, Nevia Citro, Mikael E Trellet, Li C Xue, Alexandre M J J Bonvin
Published in: Bioinformatics, Issue 35/9, 2018, Page(s) 1585-1587, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty816

DFFR: A NEW METHOD FOR HIGH-THROUGHPUT RECALIBRATION OF AUTOMATIC FORCE-FIELDS FOR DRUGS

Author(s): David Moreno, Sanja Zivanovic, Francesco Colizzi, Adam Hospital, Juan Aranda, Robert Soliva, Modesto Orozco
Published in: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c00306

Large scale relative protein ligand binding affinities using non-equilibrium alchemy

Author(s): Vytautas Gapsys, Laura Pérez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L. de Groot
Published in: Chemical Science, Issue 11/4, 2020, Page(s) 1140-1152, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sc03754c

Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope

Author(s): Laura Orellana, Amy H. Thorne, Rafael Lema, Johan Gustavsson, Alison D. Parisian, Adam Hospital, Tiago N. Cordeiro, Pau Bernadó, Andrew M. Scott, Isabelle Brun-Heath, Erik Lindahl, Webster K. Cavenee, Frank B. Furnari, Modesto Orozco
Published in: Proceedings of the National Academy of Sciences, Issue 116/20, 2019, Page(s) 10009-10018, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1821442116

MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

Author(s): Jógvan Magnus Haugaard Olsen, Viacheslav Bolnykh, Simone Meloni, Emiliano Ippoliti, Martin P. Bircher, Paolo Carloni, Ursula Rothlisberger
Published in: Journal of Chemical Theory and Computation, Issue 15/6, 2019, Page(s) 3810-3823, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.9b00093

PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes

Author(s): Brian Jiménez-García, Katarina Elez, Panagiotis I Koukos, Alexandre Mjj Bonvin, Anna Vangone
Published in: Bioinformatics, Issue 35/22, 2019, Page(s) 4821-4823, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz437

Molecular Dynamics Simulation of Amorphous Poly(3-hexylthiophene)

Author(s): Flora D. Tsourtou, Loukas D. Peristeras, Rossen Apostolov, Vlasis G. Mavrantzas
Published in: Macromolecules, 2020, ISSN 0024-9297
Publisher: American Chemical Society
DOI: 10.1021/acs.macromol.0c00454

iScore: a novel graph kernel-based function for scoring protein–protein docking models

Author(s): Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant Honavar, Alexandre M J J Bonvin, Li C Xue
Published in: Bioinformatics, Issue 36/1, 2019, Page(s) 112-121, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz496

Structural biology in the clouds: The WeNMR-EOSC Ecosystem.

Author(s): R. Vargas Honorato, P.I. Koukos, B. Jimenez-Garcia, A. Tsaregorodtsev, M. Verlato, A. Giachetti, A. Rosato and A.M.J.J. Bonvin.
Published in: Frontiers in Molecular Biosciences, Issue 8, 2021, ISSN 2296-889X
Publisher: Frontiers Media S.A.
DOI: 10.3389/fmolb.2021.729513

Molecular Basis of CLC Antiporter Inhibition by Fluoride.

Author(s): Maria Gabriella Chiariello; Viacheslav Bolnykh; Emiliano Ippoliti; Simone Meloni; Jógvan Magnus Haugaard Olsen; Thomas L. Beck; Ursula Rothlisberger; Christoph Fahlke; Paolo Carloni
Published in: JACS, Issue 67, 2020, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.9b13588

Accurate Calculation of Free Energy Changes upon Amino Acid Mutation

Author(s): Matteo Aldeghi, Bert L. de Groot, Vytautas Gapsys
Published in: Computational Methods in Protein Evolution, Issue 1851, 2019, Page(s) 19-47, ISBN 978-1-4939-8735-1
Publisher: Springer New York
DOI: 10.1007/978-1-4939-8736-8_2

Managing Failures in Task-Based Parallel Workflows in Distributed Computing Environments

Author(s): Jorge Ejarque, Marta Bertran, Javier Álvarez Cid-Fuentes, Javier Conejero, Rosa M. Badia
Published in: Euro-Par 2020: Parallel Processing - 26th International Conference on Parallel and Distributed Computing, Warsaw, Poland, August 24–28, 2020, Proceedings, Issue 12247, 2020, Page(s) 411-425, ISBN 978-3-030-57674-5
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-57675-2_26

Protein–Protein Modeling Using Cryo-EM Restraints

Author(s): Mikael Trellet, Gydo van Zundert, Alexandre M. J. J. Bonvin
Published in: Structural Bioinformatics - Methods and Protocols, Issue 2112, 2020, Page(s) 145-162, ISBN 978-1-0716-0269-0
Publisher: Springer US
DOI: 10.1007/978-1-0716-0270-6_11

A protocol for information-driven antibody-antigen modelling with the HADDOCK2.4 webserver

Author(s): F. Ambrosetti, Zuzana Jandova and A.M.J.J. Bonvin
Published in: 2020
Publisher: arvix
DOI: 10.48550/arXiv.2005.03283

proABC-2: PRediction Of AntiBody Contacts v2 and its application to information-driven docking

Author(s): F. Ambrosetti, T.H. Olsed, P.P. Olimpieri, B. Jiménez-García, E. Milanetti, P. Marcatilli and A.M.J.J. Bonvin
Published in: bioRxiv, 2020, ISSN 0362-4331
Publisher: New York Times Company
DOI: 10.1101/2020.03.18.967828

Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

Author(s): V. Gapsys and B.L. de Groot
Published in: 2019, ISSN 2050-084X
Publisher: eLife: Accelerating discovery
DOI: 10.7554/elife.44718.001

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